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[hal-04292325] At the interfaces of the hydrologic sciences: Connecting water, elements, ecosystems, and people through the major contributions of Dr. Emily Bernhardt
this paper, we describe the major contributions of Professor Emily Bernhardt to the hydrologic sciences. Dr. Bernhardt's work addresses how carbon, nutrient, and contaminant dynamics respond to a wide range of environmental perturbations that alter hydrologic dynamics within and connectivity among ecosystems. Her research leverages intensive and extensive field sampling, experimental manipulations, macroscale data harmonization and exploration, and continental to global-scale synthesis activities to uncover key drivers and patterns of the impacts human perturbations have on water and elemental cycles. Dr. Bernhardt's research program is defined by her ability to ask questions and use approaches that explicitly consider connectivity and interfaces in a variety of ways. Here, we highlight significant contributions from Dr. Bernhardt's work, organized by connectivity, interfaces, and interactions among and across (1) elemental cycles, (2) ecosystems, (3) water-sheds, (4) scales, and (5) disciplines. We conclude with a section on Dr. Bernhardt's impact on the hydrologic sciences and beyond through her exceptional dedication to mentorship, engagement, and service.
ano.nymous@ccsd.cnrs.fr.invalid (Ashley Helton) 17 Nov 2023
https://hal.inrae.fr/hal-04292325v1
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[hal-04914263] Century-old herbarium specimen provides insights into Pierce’s disease of grapevines emergence in the Americas
Fossils and other preserved specimens are integral for informing timing and evolutionary history in every biological system. By isolating a plant pathogen genome from herbarium-preserved diseased grapevine material from 1906 (Herb_1906), we were able to answer questions about an enigmatic system. The emergence of Pierce’s disease (PD) of grapevine has shaped viticultural production in North America; yet, there are uncertainties about the geographic origin of the pathogen (Xylella fastidiosa subsp. fastidiosa, Xff) and the timing and route of its introduction. We produced a high-quality, de novo genome assembly of this historical plant pathogen and confirmed degradation patterns unique to ancient DNA. Due to the inclusion of the Herb_1906 sample, we were able to generate a significant temporal signal in the genomic data. This allowed us to build a time-calibrated phylogeny, where we estimate the introduction of Xff into the US between 1734 and 1741 CE, an earlier time frame than previously inferred. In a large collection of >300 Xff genomes, the Herb_1906 sample was genetically most similar to a small population from Northern California but not basal to the entire Xff California clade. Based on phylogenetic placement and a phylogeographic reconstruction, our data support a single introduction of Xff into the Southeastern US from Central America, with multiple subsequent introductions into California.
ano.nymous@ccsd.cnrs.fr.invalid (Monica Donegan) 27 Jan 2025
https://hal.science/hal-04914263v1
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[hal-05056340] Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth
High proliferation rate and robustness are vital characteristics of bacterial pathogens that successfully colonize their hosts. The observation of drastically slow growth in some pathogens is thus paradoxical and remains unexplained. In this study, we sought to understand the slow (fastidious) growth of the plant pathogen Xylella fastidiosa. Using genome-scale metabolic network reconstruction, modeling, and experimental validation, we explored its metabolic capabilities. Despite genome reduction and slow growth, the pathogen's metabolic network is complete but strikingly minimalist and lacking in robustness. Most alternative reactions were missing, especially those favoring fast growth, and were replaced by less efficient paths. We also found that the production of some virulence factors imposes a heavy burden on growth. Interestingly, some specific determinants of fastidious growth were also found in other slow-growing pathogens, enriching the view that these metabolic peculiarities are a pathogenicity strategy to remain at a low population level. IMPORTANCE Xylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe. A main challenge for the detection of the pathogen and the development of physiological studies is its fastidious growth, as the generation time can vary from 10 to 100 h for some strains. This physiological peculiarity is shared with several human pathogens and is poorly understood. We performed an analysis of the metabolic capabilities of X. fastidiosa through a genome-scale metabolic model of the bacterium. This model was reconstructed and manually curated using experiments and bibliographical evidence. Our study revealed that fastidious growth most probably results from different metabolic specificities such as the absence of highly efficient enzymes or a global inefficiency in virulence factor production. These results support the idea that the fragility of the metabolic network may have been shaped during evolution to lead to the self-limiting behavior of X. fastidiosa.
ano.nymous@ccsd.cnrs.fr.invalid (Léo Gerlin) 13 May 2025
https://hal.inrae.fr/hal-05056340v1
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[hal-05056253] Draft genome sequences of five Pseudomonas syringae pv. actinidifoliorum strains isolated in France
Pseudomonas syringae pv. actinidifoliorum causes necrotic spots on the leaves of Actinidia deliciosa and Actinidia chinensis. P. syringae pv. actinidifoliorum has been detected in New Zealand, Australia, France and Spain. Four lineages were previously identified within the P. syringae pv. actinidifoliorum species group. Here, we report the draft genome sequences of five strains of P. syringae pv. actinidifoliorum representative of lineages 1, 2 and 4, isolated in France. The whole genomes of strains isolated in New Zealand, representative of P. syringae pv. actinidifoliorum lineages 1 and 3, were previously sequenced. The availability of supplementary P. syringae pv. actinidifoliorum genome sequences will be useful for developing molecular tools for pathogen detection and for performing comparative genomic analyses to study the relationship between P. syringae pv. actinidifoliorum and other kiwifruit pathogens, such as P. syringae pv. actinidiae. (C) 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. This is an open access article under the CC BY-NC-ND license
ano.nymous@ccsd.cnrs.fr.invalid (Amandine Cunty) 09 May 2025
https://hal.science/hal-05056253v1
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[hal-05081398] A cross-systems primer for synthetic microbial communities
The design and use of synthetic communities, or SynComs, is one of the most promising strategies for disentangling the complex interactions within microbial communities, and between these communities and their hosts. Compared to natural communities, these simplified consortia provide the opportunity to study ecological interactions at tractable scales, as well as facilitating reproducibility and fostering interdisciplinary science. However, the effective implementation of the SynCom approach requires several important considerations regarding the development and application of these model systems. There are also emerging ethical considerations when both designing and deploying SynComs in clinical, agricultural or environmental settings. Here we outline current best practices in developing, implementing and evaluating SynComs across different systems, including a focus on important ethical considerations for SynCom research. Here the authors outline best practices for the development, implementation and evaluation of synthetic microbial communities (or SynComs) across different systems.
ano.nymous@ccsd.cnrs.fr.invalid (Elijah Mehlferber) 23 May 2025
https://hal.inrae.fr/hal-05081398v1
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[hal-05081372] Sowing success: ecological insights into seedling microbial colonisation for robust plant microbiota engineering
Manipulating the seedling microbiota through seed or soil inoculations has the potential to improve plant health. Mixed in-field results have been attributed to a lack of consideration for ecological processes taking place during seedling micro- biota assembly. In this opinion article, we (i) assess the contribution of ecological processes at play during seedling microbiota assembly (e.g., propagule pressure and priority effects); (ii) investigate how life history theory can help us identify microbial traits involved in successful seedling colonisation; and (iii) suggest how different plant microbiota engineering methods could benefit from a greater understanding of seedling microbiota assembly processes. Finally, we propose several research hypotheses and identify outstanding questions for the plant microbiota engineering community.
ano.nymous@ccsd.cnrs.fr.invalid (Oscar Joubert) 23 May 2025
https://hal.inrae.fr/hal-05081372v1
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[hal-05056273] Phylogenetic and Variable-Number Tandem-Repeat Analyses Identify Nonpathogenic Xanthomonas arboricola Lineages Lacking the Canonical Type III Secretion System
ABSTRACT Xanthomonas arboricola is conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. This study showed that X. arboricola also encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. The aim of this study was to assess the X. arboricola population structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. A multilocus sequence analysis (MLSA) was performed on a collection of 100 X. arboricola strains, including 27 nonpathogenic strains isolated from walnut. Nonpathogenic strains grouped outside clusters defined by pathovars and formed separate genetic lineages. A multilocus variable-number tandem-repeat analysis (MLVA) conducted on a collection of X. arboricola strains isolated from walnut showed that nonpathogenic strains clustered separately from clonal complexes containing Xanthomonas arboricola pv. juglandis strains. Some nonpathogenic strains of X. arboricola did not contain the canonical type III secretion system (T3SS) and harbored only one to three type III effector (T3E) genes. In the nonpathogenic strains CFBP 7640 and CFBP 7653, neither T3SS genes nor any of the analyzed T3E genes were detected. This finding raises a question about the origin of nonpathogenic strains and the evolution of plant pathogenicity in X. arboricola . T3E genes that were not detected in any nonpathogenic isolates studied represent excellent candidates to be those responsible for pathogenicity in X. arboricola .
ano.nymous@ccsd.cnrs.fr.invalid (Salwa Essakhi) 05 May 2025
https://hal.science/hal-05056273v1
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[hal-05056294] Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Cesbron) 05 May 2025
https://hal.science/hal-05056294v1
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[hal-05056348] Development of A Nested-MultiLocus Sequence Typing Approach for A Highly Sensitive and Specific Identification of Xylella fastidiosa Subspecies Directly from Plant Samples
Identification of sequence types (ST) of Xylella fastidiosa based on direct MultiLocus Sequence Typing (MLST) of plant DNA samples is partly efficient. In order to improve the sensitivity of X. fastidiosa identification, we developed a direct nested-MLST assay on plant extracted DNA. This method was performed based on a largely used scheme targeting seven housekeeping gene (HKG) loci (cysG, gltT, holC, leuA, malF, nuoL, petC). Samples analyzed included 49 plant species and two insect species (Philaenus spumarius, Neophilaenus campestris) that were collected in 2017 (106 plant samples in France), in 2018 (162 plant samples in France, 40 plant samples and 26 insect samples in Spain), and in 2019 (30 plant samples in Spain). With the nested approach, a significant higher number of samples were amplified. The threshold was improved by 100 to 1000 times compared to conventional PCR. Using nested-MLST assay, plants that were not yet considered hosts tested positive and revealed novel alleles in France, whereas for Spanish samples it was possible to assign the subspecies or ST to samples considered as new hosts in Europe. Direct typing by nested-MLST from plant material has an increased sensitivity and may be useful for epidemiological purposes.
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Cesbron) 14 May 2025
https://hal.inrae.fr/hal-05056348v1
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[hal-05056275] Niches and routes of transmission of Xanthomonas citri pv. fuscans to bean seeds
Seeds are vectors of a diversified microbiota including plant pathogens. To better understand transmission of common bacterial blight (CBB) agents to bean seeds, we analyzed the role of non-pathogenic xanthomonads on seed transmission efficiency and investigated the location of Xanthomonas citri pv. fuscans (Xcf) into seeds and plantlets. Competition between CBB and NP strains was initially assessed in vitro and then extended in planta to monitor the impact of co-inoculation on Xcf seed transmission. Moreover, location of Xcf strains in seeds and seedlings was visualized using a combination of gfp-tagged strain and DOPE-FISH/CSLM. Whereas CBB agent growth was inhibited in vitro by some seed-borne non-pathogenic xanthomonads strains, these strains did not transmit efficiently to seed through floral pathway and did not affect Xcf seed transmission. Xcf cells were observed entering seed through vascular elements and parenchyma of funiculus, but also micropyle and testa. Xcf cells were observed, moreover, among other bacteria on radicle surfaces, especially tip, in cotyledons, and plumules. CBB agents are more efficient than non-pathogenic xanthomonads in using the floral route to colonize seeds. CBB agents are located within different niches in the seed tissues up to the embryonic axis.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 05 May 2025
https://univ-angers.hal.science/hal-05056275v1
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[hal-05056279] Clavibacter michiganensis subsp. michiganensis strains from central Chile exhibit low genetic diversity and sequence types match strains in other parts of the world
Bacterial canker caused by Clavibacter michiganensis subsp. michiganensis (Cmm) is one of the most important bacterial diseases of tomato. In order to understand the emergence and dissemination of this pathogen in Chile, Chilean Cmm strains isolated from different sites in central Chile were characterized and compared to a worldwide collection of strains. Multilocus sequence analysis and typing ( MLSA ‐ MLST ) based on five housekeeping genes, i.e. atpD , dnaK , gyrB , ppk and recA , and multilocus variable number of tandem repeats ( VNTR ) analysis ( MLVA ) based on eight VNTR s were used. Low diversity was found using MLSA ‐ MLST among the 25 Chilean strains, which clustered into three groups, each corresponding to a single sequence type ( ST ). Group I contained most strains (21/25), isolated over different years from Valparaíso and O'Higgins regions. Group II contained only one strain from Maule region that was isolated in 2005. These two groups belonged to the same genetic lineage. Group III contained three strains from Valparaíso region isolated in 2004, 2012 and 2013. MLVA also distributed the strains into the same three groups. Group III strains shared the same ST as strains from Algeria, Belgium, France, the Netherlands, Uruguay and the USA . Group II strains shared the same ST as strains from Brazil and Uruguay, while Group I strains shared the same ST as two strains of unknown origin. This study shows that Cmm strains from central Chile tend to be clonal and have similar genetic profiles to strains from other countries.
ano.nymous@ccsd.cnrs.fr.invalid (M. Valenzuela) 05 May 2025
https://hal.inrae.fr/hal-05056279v1
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[hal-02901652] Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth
High proliferation rate and robustness are vital characteristics of bacterial pathogens that successfully colonize their hosts. The observation of drastically slow growth in some pathogens is thus paradoxical and remains unexplained. In this study, we sought to understand the slow (fastidious) growth of the plant pathogen Xylella fastidiosa. Using genome-scale metabolic network reconstruction, modeling, and experimental validation, we explored its metabolic capabilities. Despite genome reduction and slow growth, the pathogen's metabolic network is complete but strikingly minimalist and lacking in robustness. Most alternative reactions were missing, especially those favoring fast growth, and were replaced by less efficient paths. We also found that the production of some virulence factors imposes a heavy burden on growth. Interestingly, some specific determinants of fastidious growth were also found in other slow-growing pathogens, enriching the view that these metabolic peculiarities are a pathogenicity strategy to remain at a low population level.IMPORTANCE Xylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe. A main challenge for the detection of the pathogen and the development of physiological studies is its fastidious growth, as the generation time can vary from 10 to 100 h for some strains. This physiological peculiarity is shared with several human pathogens and is poorly understood. We performed an analysis of the metabolic capabilities of X. fastidiosa through a genome-scale metabolic model of the bacterium. This model was reconstructed and manually curated using experiments and bibliographical evidence. Our study revealed that fastidious growth most probably results from different metabolic specificities such as the absence of highly efficient enzymes or a global inefficiency in virulence factor production. These results support the idea that the fragility of the metabolic network may have been shaped during evolution to lead to the self-limiting behavior of X. fastidiosa.
ano.nymous@ccsd.cnrs.fr.invalid (Léo Gerlin) 13 May 2025
https://hal.inrae.fr/hal-02901652v1
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[hal-05056260] Development of multilocus variable-number tandem repeat analysis (MLVA) for Xanthomonas arboricola pathovars
Xanthomonas arboricola is an important bacterial species, the pathovars of which are responsible for bacterial blight diseases on stone fruit, hazelnut, Persian walnut, poplar, strawberry, poinsettia and banana. In this study, we evaluated variable number tandem repeats (VNTR) as a molecular typing tool for assessing the genetic diversity within pathovars of X. arboricola. Screening of the X. arboricola pv. pruni genome sequence (CFBP5530 strain) predicted 51 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 51 loci were designed, and their discriminatory power was initially evaluated with a core collection of 8 X. arboricola strains representative of the different pathovars. Next, the 26 polymorphic VNTR loci present in all strains were used for genotyping a collection of 61 strains. MLVA is a typing method that clearly differentiates X. arboricola strains. The MLVA scheme described in this study is a rapid and reliable molecular typing tool that can be used for further epidemiological studies of bacterial diseases caused by X. arboricola pathovars. (C) 2014 Elsevier B.V. All rights reserved.
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Cesbron) 05 May 2025
https://hal.inrae.fr/hal-05056260v1
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[hal-05056226] From insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic <i>Arsenophonus</i> strains
Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens "Candidatus Arsenophonus phytopathogenicus" (Ap) and "Ca. Phlomobacter fragariae" (Pf ) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the "Triatominarum" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopatho genicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.
ano.nymous@ccsd.cnrs.fr.invalid (Mathieu Mahillon) 05 May 2025
https://hal.inrae.fr/hal-05056226v1
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[hal-05056292] Origin of the Outbreak in France of Pseudomonas syringae pv. actinidiae Biovar 3, the Causal Agent of Bacterial Canker of Kiwifruit, Revealed by a Multilocus Variable-Number Tandem-Repeat Analysis
ABSTRACT The first outbreaks of bacterial canker of kiwifruit caused by Pseudomonas syringae pv. actinidiae biovar 3 were detected in France in 2010. P. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. P. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. In order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in France, we developed a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA). MLVA was conducted on 340 strains of P. syringae pv. actinidiae biovar 3 isolated in Chile, China, France, Italy, and New Zealand and on 39 strains of P. syringae pv. actinidifoliorum isolated in Australia, France, and New Zealand. Eleven polymorphic VNTR loci were identified in the genomes of P. syringae pv. actinidiae biovar 3 ICMP 18744 and of P. syringae pv. actinidifoliorum ICMP 18807. MLVA enabled the structuring of P. syringae pv. actinidiae biovar 3 and P. syringae pv. actinidifoliorum strains in 55 and 16 haplotypes, respectively. MLVA and discriminant analysis of principal components revealed that strains isolated in Chile, China, and New Zealand are genetically distinct from P. syringae pv. actinidiae strains isolated in France and in Italy, which appear to be closely related at the genetic level. In contrast, no structuring was observed for P. syringae pv. actinidifoliorum. We developed an MLVA scheme to explore the diversity within P. syringae pv. actinidiae biovar 3 and to trace the dispersal routes of epidemic P. syringae pv. actinidiae biovar 3 in Europe. We suggest using this MLVA scheme to trace the dispersal routes of P. syringae pv. actinidiae at a global level.
ano.nymous@ccsd.cnrs.fr.invalid (A. Cunty) 05 May 2025
https://hal.inrae.fr/hal-05056292v1
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[hal-05056282] First report of tomato bacterial speck caused by Pseudomonas syringae pv. tomato in Tunisia
[...]
ano.nymous@ccsd.cnrs.fr.invalid (I. Mensi) 05 May 2025
https://hal.inrae.fr/hal-05056282v1
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[hal-05056297] The alternative Ï factor HrpL negatively modulates the flagellar system in the phytopathogenic bacterium Erwinia amylovora under hrp -inducing conditions
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Sophie Cesbron) 05 May 2025
https://hal.inrae.fr/hal-05056297v1
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[hal-05056301] Adhesion and Fitness in the Bean Phyllosphere and Transmission to Seed of Xanthomonas fuscans subsp. fuscans
Deciphering the mechanisms enabling plant-pathogenic bacteria to disperse, colonize, and survive on their hosts provides the necessary basis to set up new control methods. We evaluated the role of bacterial attachment and biofilm formation in host colonization processes for Xanthomonas fuscans subsp. fuscans on its host. This bacterium is responsible for the common bacterial blight of bean (Phaseolus vulgaris), a seedborne disease. The five adhesin genes (pilA, fhab, xadA1, xadA2, and yapH) identified in X. fuscans subsp. fuscans CFBP4834-R strain were mutated. All mutants were altered in their abilities to adhere to polypropylene or seed. PilA was involved in adhesion and transmission to seed, and mutation of pilA led to lower pathogenicity on bean. YapH was required for adhesion to seed, leaves, and abiotic surfaces but not for in planta transmission to seed or aggressiveness on leaves. Transmission to seed through floral structures did not require any of the known adhesins. Conversely, all mutants tested, except in yapH, were altered in their vascular transmission to seed. In conclusion, we showed that adhesins are implicated in the various processes leading to host phyllosphere colonization and transmission to seed by plant-pathogenic bacteria.
ano.nymous@ccsd.cnrs.fr.invalid (A. Darsonval) 05 May 2025
https://hal.inrae.fr/hal-05056301v1
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[hal-05056361] Molecular characterization of Algerian Erwinia amylovora strains by VNTR analysis and biocontrol efficacy of Bacillus spp. and Pseudomonas brassicacearum antagonists
Destructive Xylella fastidiosa ( Xf ) outbreaks in Europe highlight this pathogen’s capacity to expand its host range and geographical distribution. The current disease diagnostic approaches are limited by a multiple-step process, biases to known sequences, and detection limits.
ano.nymous@ccsd.cnrs.fr.invalid (Verónica Román-Reyna) 05 May 2025
https://hal.inrae.fr/hal-05056361v1
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[hal-05056287] Novel Tetraplex Quantitative PCR Assays for Simultaneous Detection and Identification of Xylella fastidiosa Subspecies in Plant Tissues
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Enora Dupas) 05 May 2025
https://hal.inrae.fr/hal-05056287v1
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[hal-03834661] Single seed microbiota: assembly and transmission from parent plant to seedling
The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 05 Sep 2024
https://hal.inrae.fr/hal-03834661v1
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[hal-04665509] A stage‐dependent seed defense response to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean
Although seed represents an important means of plant pathogen dispersion, the seed–pathogen dialogue remains largely unexplored. A multiomic approach was performed at different seed developmental stages of common bean ( Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans ( Xcf ), At the early seed developmental stages, we observed high transcriptional changes both in seeds with bacterial recognition and defense signal transduction genes, and in bacteria with up‐regulation of the bacterial type 3 secretion system. This high transcriptional activity of defense genes in Xcf ‐colonized seeds during maturation refutes the widely diffused assumption considering seeds as passive carriers of microbes. At later seed maturation stages, few transcriptome changes indicated a less intense molecular dialogue between the host and the pathogen, but marked by changes in DNA methylation of plant defense genes, in response to Xcf colonization. We showed examples of pathogen‐specific DNA methylations in colonized seeds acting as plant defense silencing to repress plant immune response during the germination process. Finally, we propose a novel plant–pathogen interaction model, specific to the seed tissues, highlighting the existence of distinct phases during seed–pathogen interaction with seeds being actively interacting with colonizing pathogens, then both belligerents switching to more passive mode at later stages.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 31 Jul 2024
https://hal.inrae.fr/hal-04665509v1
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[hal-04579728] Interactions shape aquatic microbiome responses to Cu and Au nanoparticle treatments in wetland manipulation experiments
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Zhao Wang) 18 May 2024
https://hal.science/hal-04579728v1
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[hal-04208811] Seasonal Differences and Grazing Pressure Alter the Fate of Gold Nanoparticles in a Microcosm Experiment
Gold nanoparticles (AuNPs) are used as models to track and predict NP fates and effects in ecosystems. Previous work found that aquatic macrophytes and their associated biofilm primarily drove the fate of AuNPs within aquatic ecosystems and that seasonality was an important abiotic factor in the fate of AuNPs. Therefore, the present work aims to study if grazers, by feeding on these interfaces, modify the AuNP fate and if this is altered by seasonal fluctuations. Microcosms were dosed with 44.8 mu g/L of AuNP weekly for 4 weeks and maintained in environmental chambers simulating Spring and Fall light and temperature conditions. We discovered that seasonal changes and the presence of grazers significantly altered the fate of Au. Higher temperatures in the warmer season increased dissolved organic carbon (DOC) content in the water column, leading to stabilization of Au in the water column. Additionally, snail grazing on biofilm growing on the Egeria densa surface led to a transfer of Au from macrophytes to the organic matter above the sediments. These results demonstrate that climate and grazers significantly impacted the fate of Au from AuNPs, highlighting the role that grazers might have in a large and biologically more complex ecosystem.
ano.nymous@ccsd.cnrs.fr.invalid (Christina Bergemann) 20 Dec 2023
https://hal.science/hal-04208811v1
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[hal-04528599] Characterisation of the spermosphere of the common bean seed (Phaseolus vulgaris)
Seed plants have co-evoluted with microorganisms by forming beneficial relationships in order to facilitate their adaptation to terrestrial lifestyle. Indeed, more and more studies are demonstrating the inter-relationships of the microbiome and their hosts and the resulting impacts of such relationships in terms of the host’s fitness, environmental response, adaptation and evolution. These studies have given rise to a relatively new concept of the holobiont which views the host organism and its associated microbiota as a single functional unit, where evolutionary selection occurs between both the host and its microbiota, as well as among different microbial species within the microbiota. While plant microbiome in the phyllosphere and rhizosphere has been well studied, seed spermosphere and microbiome have remain relatively unnoticed. Yet, seeds have an important distinctive function in the inheritance process by connecting plant generations and serving as a critical point in the continuity of the plant microbiome. However, the fate of seed-borne microorganisms after germination is relatively unexplored. Seed germination, a transient process giving rise to a microenvironment known as the spermosphere, is a critical point for the establishment of the future plant microbiome. Indeed, seed exudation after imbibition is hypothesized to be the driving force for microbial selection, growth and interaction in the spermosphere. The aim of this study is to characterize the germinating bean spermosphere with multi-omics technologies to understand the complex interactions between seed borne microorganisms and seed exudates
ano.nymous@ccsd.cnrs.fr.invalid (Chandrodhay Saccaram) 01 Apr 2024
https://hal.science/hal-04528599v1
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[hal-04688340] Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress
Microbiota that originate in the seed can have consequences for the education of the plant immune system, competitive exclusion of pathogens from the host tissue, and host access to critical nutrients. Our research objective was to investigate the consequences of the environmental conditions of the parent plant for bacterial seed microbiome assembly and transmission across plant generations. Using a fully facto rial, three-generational experimental design, we investigated endophytic seed bacterial communities of common bean lines ( Phaseolus vulgaris L.) grown in the growth chamber and exposed to either control conditions, drought, or excess nutrients at each genera tion. We applied 16S rRNA microbiome profiling to the seed endophytes and measured plant health outcomes. We discovered stable transmission of 22 bacterial members, regardless of the parental plant condition. This study shows the maintenance of bacterial members of the plant microbiome across generations, even under environmental stress. Overall, this work provides insights into the ability of plants to safeguard microbiome members, which has implications for crop microbiome management in the face of climate change. IMPORTANCE Seed microbiomes initiate plant microbiome assembly and thus have critical implications for the healthy development and performance of crops. However, the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown, but this is critical information, given the intensifying stressors that crops face as the climate crisis accelerates. This study provides insights into the maintenance of plant microbiomes across generations, with implica tions for durable plant microbiome maintenance in agriculture on the changing planet.
ano.nymous@ccsd.cnrs.fr.invalid (Abby Sulesky-Grieb) 05 Sep 2024
https://hal.inrae.fr/hal-04688340v1
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[hal-04599898] Terroir, baker’s practices, wheat varieties and their influence on sourdough microbial diversity
The microbial diversity of many ecosystems has recently been described but the question remains of the extent to which species and varieties develop and evolve within their particular environments. Altenatively, are they essentially ubiquitous, being more frequent in certain localities as a result of the conditions encountered? Is the distribution geographically structured, and/or influenced by other factors ? Using sourdough breadmaking ecosystems as a model and participatory research approach, we are analysing human influence on the dispersion and selection of lactic acid bacteria and yeasts. In France, microbial diversity associated with bread-making has not been well-documented. Bread can be made by two kind of artisans, farmer-bakers and artisan-bakers. Both use sourdough to leaven the bread. Sourdough is a dough composed of wheat and rye flour, or only one of these two ingredients, water, possibly supplemented with salt and subjected to an acidifying natural fermentation, whose function is to ensure the dough raising Décret No. 93- 1074, 13 sept. 1993). This aim of this study was to describe diversity of microbial species in baker's sourdough (yeasts and lactic acid bacteria) and to understand the evolutionary process (dispersion, selection) that shape this diversity.
ano.nymous@ccsd.cnrs.fr.invalid (Elisa Michel) 04 Jun 2024
https://hal.inrae.fr/hal-04599898v1
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[inserm-04492349] Emergence and spread of Mycobacterium ulcerans at different geographic scales
ABSTRACT The classical lineage of Mycobacterium ulcerans is the most prevalent clonal group associated with Buruli ulcer in humans. Its reservoir is strongly associated with the environment. We analyzed together 1,045 isolates collected from 13 countries on two continents to define the evolutionary history and population dynamics of this lineage. We confirm that this lineage spread over 7,000 years from Australia to Africa with the emergence of outbreaks in distinct waves in the 18th and 19th centuries. In sharp contrast with its global spread over the last century, transmission chains are now mostly local, with little or no dissemination between endemic areas. This study provides new insights into the phylogeography and population dynamics of M. ulcerans, highlighting the importance of comparative genomic analyses to improve our understanding of pathogen transmission. IMPORTANCE Mycobacterium ulcerans is an environmental mycobacterial pathogen that can cause Buruli ulcer, a severe cutaneous infection, mostly spread in Africa and Australia. We conducted a large genomic study of M. ulcerans , combining genomic and evolutionary approaches to decipher its evolutionary history and pattern of spread at different geographic scales. At the scale of villages in an endemic area of Benin, the circulating genotypes have been introduced in recent decades and are not randomly distributed along the river. On a global scale, M. ulcerans has been spreading for much longer, resulting in distinct and compartmentalized endemic foci across Africa and Australia.
ano.nymous@ccsd.cnrs.fr.invalid (Martial Briand) 28 Mar 2024
https://inserm.hal.science/inserm-04492349v1
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[hal-05015613] CIRM-CFBP : Plan de Gestion des Données
Plan de Gestion des Données du CIRM-CFBP. Le CIRM est un Groupement d'Intérêt Scientifique (GIS) créé en 2004 par INRAE autour de ses collections de micro-organismes (bactéries, levures et champignons filamenteux). Il est Coordonné par INRAE et est constitué de cinq centres de ressources biologique (CRB), tous certifiés ISO 9001. Ces CRB conservent plus de 22 000 souches de bactéries associées aux plantes, bactéries pathogènes, bactéries d'intérêt alimentaire, levures et champignons filamenteux. Le CIRM est labellisé « ISC », Infrastructure Scientifique de Recherche par l’IR RARe. Le CIRM-CFBP est le CRB dédié aux bactéries associées aux plantes. Il est accueilli à l'UMR 1345 IRHS. INRAE.
ano.nymous@ccsd.cnrs.fr.invalid (Perrine Portier) 01 Apr 2025
https://hal.inrae.fr/hal-05015613v1
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[hal-04688338] Alkaline mine drainage drives stream sediment microbial community structure and function
With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and functional responses of microbial communities in different environmental compartments are not well understood. We investigated sediment microbiomes in mining impacted streams to determine how community composition and function respond to mining and to look for potential microbial bioindicators. Using 16s rRNA gene amplicon sequencing, we found that mining leads to shifts in microbial community structure, with the phylum Planctomycetes enriched by 1-6% at mined sites. We observed ~51% increase in species richness in bulk sediments. In contrast, of the 31 predicted metabolic pathways that changed significantly with mining, 23 responded negatively. Mining explained 15-18% of the variance in community structure and S, Se, %C and %N were the main drivers of community and functional pathway composition. We identified 12 microbial indicators prevalent in the ecosystem and sensitive to mining. Overall, alkaline mountaintop mining drainage causes a restructuration of the sediment microbiome, and our study identified promising microbial indicators for the long-term monitoring of these impacted streams.
ano.nymous@ccsd.cnrs.fr.invalid (Lingrong Jin) 05 Sep 2024
https://hal.inrae.fr/hal-04688338v1
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[hal-02941967] Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 30 Dec 2023
https://hal.inrae.fr/hal-02941967v1
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[hal-04111816] Chronic Engineered Nanoparticle Additions Alter Insect Emergence and Result in Metal Flux from Aquatic Ecosystems into Riparian Food Webs
Freshwater ecosystems are exposed to engineered nanoparticles (NPs) through discharge from wastewater and agricultural runoff. We conducted a 9-month mesocosm experiment to examine the combined effects of chronic NP additions on insect emergence and insect-mediated contaminant flux to riparian spiders. Two NPs (copper, gold, plus controls) were crossed by two levels of nutrients in 18 outdoor mesocosms open to natural insect and spider colonization. We collected adult insects and two riparian spider genera, Tetragnatha and Dolomedes, for 1 week on a monthly basis. We estimated a significant decrease in cumulative insect emergence of 19% and 24% after exposure to copper and gold NPs, irrespective of nutrient level. NP treatments led to elevated copper and gold tissue concentrations in adult insects, which resulted in terrestrial fluxes of metals. These metal fluxes were associated with increased gold and copper tissue concentrations for both spider genera. We also observed about 25% fewer spiders in the NP mesocosms, likely due to reduced insect emergence and/or NP toxicity. These results demonstrate the transfer of NPs from aquatic to terrestrial ecosystems via emergence of aquatic insects and predation by riparian spiders, as well as significant reductions in insect and spider abundance in response to NP additions.
ano.nymous@ccsd.cnrs.fr.invalid (Brittany G Perrotta) 31 May 2023
https://hal.inrae.fr/hal-04111816v1
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[hal-02516590] Assembly of seed-associated microbial communities within and across successive plant generations
<p>Background and aims</p> <p>Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.</p> <p>Methods</p> <p>Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.</p> <p>Results</p> <p>Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.</p> <p>Conclusions</p> <p>These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Samir Rezki) 13 Apr 2023
https://univ-angers.hal.science/hal-02516590v1
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[hal-04665363] Molecular dialogue of plant-bacterial interactions during seed transmission
Seed is the vector of dispersion of many phytopathogenic bacteria. The molecular dialogue that is established between the plant and these microorganisms during their transmission remains largely unknown, mainly due to the technological lock of isolating bacterial RNA from infected seeds. In this project, RNA sequencing technologies were used on both plant and bacterial cells in complement to capture technologies for enrichment of specific bacterial RNA. Changes in bacterial and plant transcriptomes, but also plant methylomes were investigated during seed transmission of the plant pathogenic bacteria Xanthomonas citri pv. fuscans (Xcf) on common bean (Phaseolus vulgaris). During the seed filling stage, we observed major transcriptomic changes in both partners. In particular a concomitant differential expression of plant defense genes (e.g. serine peptidases, LRR-kinases, MAPKs, regulators such as bZIP, TIFY, AP2/ERF) and bacterial type II/type III secretion systems effectors occurred during this stage. This intense pathogenic/defense molecular dialogue at early seed developmental stage was shut down in latter stages during seed maturation, and at maturity. We also noted that at maturity, seed transmission of Xcf altered DNA methylation at more than 800 plant genomic regions. These changes included methylation changes within promoter or coding regions of genes involved in plant defense (e.g. WRKY, NB-LR or PUB13) and seed development (e.g. AGL62, FIE2 or LEA proteins). Deep-sequencing of small RNAs at the filling and mature seed stages highlighted potential miRNA (30%) and siRNA (44%) populations originated from P. vulgaris genome. The perspectives are now to integrate all these data to identify which plant miRNAs can mediate transcript repression in plant and bacterial transcriptomes and which plant siRNA can mediate change in plant methylome.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 31 Jul 2024
https://hal.inrae.fr/hal-04665363v1
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[hal-04665344] Activation of seed defenses through defense priming
Yield losses due to seedborne pathogens have a major economic impact on the global food market. We attempted to develop sustainable strategies to stimulate pathogen resistance from the seed that have a negligeable impact on seed quality parameters, such as germination rate and homogeneity. Our approach consisted in applying defense priming treatments using plant resistance inducers (PRI) such as methyl jasmonate (MeJA) and β-aminobutyric acid (BABA) on developing or mature seeds. After a first stage of technique optimization, results from tomato and bean treated seeds showed extensive transcriptome reprogramming, with a strong effect on defense pathways. To correlate these data with pathogen resistance, we analysed developing and germinating seeds treated with different PRIs and their effects on the growth of different pathogens including bacteria and fungi. First results obtained on tomato showed a marked growth inhibition on A. brassicicola from specific PRI-treated seeds, while the effect on C. michiganensis was minor. Our next step is, now, the identification of the molecules responsible of the fungistatic effect present in treated seeds.
ano.nymous@ccsd.cnrs.fr.invalid (Jerome Verdier) 31 Jul 2024
https://hal.inrae.fr/hal-04665344v1
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[tel-04688332] Pilotage du microbiote des graines pour améliorer la santé des plantes
Après une thèse au laboratoire d’Écologie Microbienne de Lyon (Université Claude Bernard Lyon 1), puis un post-doctorat de 3 ans à Duke University (NC, USA), suivi d’un post-doctorat de 9 mois à IPME (IRD, Montpellier), j’ai intégré en octobre 2019 l’équipe EmerSys de l’Institut de Recherche en Horticulture et Semences (IRHS, Angers) pour développer une thématique de recherche sur le pilotage de la composition du microbiote des semences pour améliorer la santé des plantes. Mon projet de recherche vise à caractériser la fraction du microbiote des graines qui est transmise à la plante (i.e. son inoculum primaire) et son impact sur le phénotype de la plantule. Ces connaissances fondamentales permettent d’identifier des leviers de pilotage du microbiote des graines en favorisant la présence de certains consortia microbiens ou de fonctions microbiennes permettant d’améliorer la vigueur des graines et ainsi proposer des solutions alternatives aux pesticides appliqués sur les semences. Mon projet se structure autour de 3 axes principaux, dont les principaux résultats sont détaillés dans ce document : 1) Synthèse des connaissances sur le microbiote des graines : Méta-analyse de données de metabarcoding. 2) Étude de la transmission du microbiote des graines et impact sur le phénotype de la plantule – Approche par reconstruction de microbiotes synthétiques. 3) Contribution du microbiote des graines à la fitness et productivité de la plante – études transgénérationnelles et évolution expérimentale. Dans leur ensemble, ces travaux permettent d’obtenir des résultats originaux basées sur l’utilisation de communautés synthétiques pour établir les liens entre microbiote et santé de la plante, ainsi que sur la validation (ou invalidation) expérimentale du concept d’holobionte.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 05 Sep 2024
https://hal.inrae.fr/tel-04688332v1
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[ird-04483657] Celebrating the 20th anniversary of the first Xanthomonas genome sequences – how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and helped developing novel control measures – a perspective from the French network on Xanthomonads
In this Opinion paper, members of the French Network on Xanthomonads give their personal view on what they consider to be some of the groundbreaking discoveries in the field of molecular plant pathology over the past 20 years. By celebrating the 20th anniversary of the first Xanthomonas genome sequences, they explain how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and contributed to the development of novel control measures. Collectively, such new, genomics-enabled perspective will help to ensure sustainable agriculture and conservation of our environment in the future.
ano.nymous@ccsd.cnrs.fr.invalid (Ralf Koebnik) 29 Feb 2024
https://ird.hal.science/ird-04483657v1
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[hal-04494294] Mean species responses predict effects of environmental change on coexistence
Abstract Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. Here, we show evidence that this is indeed possible. Using theoretical and simulation‐based evidence for bi‐ and tritrophic communities, we show that environmental change effects on coexistence are proportional to mean species responses and depend on how trophic levels on average interact prior to environmental change. We then benchmark our findings using relevant cases of environmental change, showing that means of temperature optima and of species sensitivities to pollution predict concomitant effects on coexistence. Finally, we demonstrate how to apply our theory to the analysis of field data, finding support for effects of land use change on coexistence in natural invertebrate communities.
ano.nymous@ccsd.cnrs.fr.invalid (Frederik de Laender) 07 Mar 2024
https://hal.inrae.fr/hal-04494294v1
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[hal-04691991] A survey of common bacterial blight in Central Brazil reveals a third Xanthomonas species infecting common bean
A survey of common bacterial blight (CBB) was conducted in common bean fields in Brazil, in the state of Goi &amp; aacute;s and in the Federal District. Isolation from symptomatic leaves on a semi-selective medium yielded yellow, mucoid colonies typical of Xanthomonas, and 161 pure cultures were obtained. PCR with specific primers for X. phaseoli pv. phaseoli and X. citri pv. fuscans was performed and confirmed the presence of both fuscans and GL2 strains of X. citri pv. fuscans and the presence of X. phaseoli pv. phaseoli. However, for 81 isolates, PCR results were negative. Housekeeping genes gyrB and rpoD sequences placed these strains in the provisionally named X. cannabis species clade, clustering pv. zinniae, pv. esculenti, and the strain Nyagatare, isolated from beans in Rwanda in 2013. The identification of a subset of 20 strains was complemented by a positive PCR with Xanthomonas-specific primers that amplify a portion of the gumD gene and the induction of hypersensitive reaction in tomato leaves within 24-48 hours. Pathogenicity was confirmed by inoculation on the French common bean cv. Flavert and the Brazilian common bean cv. BRS &amp; Aacute;rtico. Symptoms such as white spots along the leaf blade, leaf curling, and wilting developed in inoculated plants. Partial gyrB and rpoD sequences analyses revealed identity values ranging from 98.3 to 100% between the Brazilian isolates and strain Nyagatare, proposed as X. cannabis pv. phaseoli.
ano.nymous@ccsd.cnrs.fr.invalid (Bruna Alícia R. Paiva) 09 Sep 2024
https://hal.inrae.fr/hal-04691991v1
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[hal-04844057] Development of Tools to Detect and Identify Strains Belonging to the Pseudomonas syringae Species Complex Responsible for Vein Clearing of Zucchini
Vein clearing of zucchini (VCZ) is a disease caused by seedborne bacteria that affects young plants of Cucurbita pepo subsp. pepo. VCZ agents are distributed into four phylogenetic clusters within clades 2a and 2ba of phylogroup 2 of the Pseudomonas syringae species complex. All these strains are pathogenic to squash, but only certain strains can also attack melon and cucumber. Strains belonging to clades 2b and 2d are sometimes isolated from zucchini seeds but have not been associated with VCZ epidemics. Identification tools for VCZ agents are required to improve disease control. Primers were designed to implement a seven-gene multilocus sequence analysis (MLSA) scheme for a collection of 60 strains isolated from zucchini seeds. The MLSA showed a clear predominance of strains of cluster 2ba-A and the presence of VCZ strains in a fifth cluster (2ba-C). PCR tests were designed to characterize strains in the VCZ clusters, and a multiplex qPCR test was proposed to distinguish strains with a cucurbit host range extended to melon and cucumber, harboring hopZ5 and sylC, from other strains harboring avrRpt2 and sylC. Additional qPCR tests were also designed to gain insights into clade-2b and -2d strains that can be isolated from cucurbits. These tools evaluated in silico with the NCBI database and experimentally with a collection of 112 strains detected all target strains, except for the test dedicated to clade-2b strains, and excluded 96.7 to 100% of nontarget strains. These tools are intended to serve phylogenetic studies, epidemiological monitoring, and seed testing. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
ano.nymous@ccsd.cnrs.fr.invalid (Caroline Lacault) 17 Dec 2024
https://hal.inrae.fr/hal-04844057v1
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[hal-04097465] Density declines, richness increases, and composition shifts in stream macroinvertebrates
Documenting trends of stream macroinvertebrate biodiversity is challenging because biomonitoring often has limited spatial, temporal, and taxonomic scopes. We analyzed biodiversity and composition of assemblages of >500 genera, spanning 27 years, and 6131 stream sites across forested, grassland, urban, and agricultural land uses throughout the United States. In this dataset, macroinvertebrate density declined by 11% and richness increased by 12.2%, and insect density and richness declined by 23.3 and 6.8%, respectively, over 27 years. In addition, differences in richness and composition between urban and agricultural versus forested and grassland streams have increased over time. Urban and agricultural streams lost the few disturbance-sensitive taxa they once had and gained disturbance-tolerant taxa. These results suggest that current efforts to protect and restore streams are not sufficient to mitigate anthropogenic effects.
ano.nymous@ccsd.cnrs.fr.invalid (Samantha Rumschlag) 15 May 2023
https://hal.inrae.fr/hal-04097465v1
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[hal-04665483] Mise en place d’un pathosystème Brassica napus L./Alternaria brassicicola pour l’étude du déterminisme de la transmission à la semence
Le projet SUCSEED (« Stop the Use of pestiCides on Seeds by proposing alternatives », Projet Prioritaire de Recherche « Cultiver et protéger autrement » ANR 20-PCPA-0009) vise à identifier et développer des solutions de protection des semences innovantes via des approches éco-responsables. Il s’agit plus précisément de lutter contre la transmission des agents pathogènes aux semences et contre les fontes de semis. Alternaria brassicicola est un champignon nécrotrophe, responsable du « black spot » sur les plantes de la famille des Brassicacées et capable de se transmettre aux et par les graines. La contamination des semences compromet leur germination et/ou provoque le développement de symptômes sur les plantes dans la culture suivante. Il est donc essentiel de lutter contre la transmission d’A. brassicicola aux graines. Dans le contexte actuel de nécessité de réduire le recours aux fongicides, la valorisation des défenses de la plante pourrait constituer une opportunité de développement de méthodes de lutte alternative à la lutte chimique. Mais le rôle des réactions de défense de la plante, du fruit et de la graine au cours de la phase de transmission est très mal connu. Des travaux antérieurs [1] sur Arabidopsis thaliana ont mis en évidence l’existence d’un gradient de transmissibilité d’A. brassicicola selon les étages des siliques : les graines des siliques les plus âgées (situées à la base de l’inflorescence) présentent un taux de contamination par A. brassicicola plus élevé que les graines issues des siliques plus jeunes (situées en hauteur). Les raisons de l’existence de ce gradient sont mal connues, en particulier pour ce qui est du rôle des mécanismes de défense de la plante. Pourtant, les composés de défense de la plante sont supposés être déterminants pour la sévérité des symptômes de black spot sur feuille [2]. Le présent travail décrit la mise au point d’un pathosystème pour l’étude du déterminisme de la transmission d’Alternaria brassicicola aux semences de Brassica napus L. Des siliques de la hampe florale principale de plantes de colza ont été inoculées par dépôt de gouttes contenant une suspension de conidies d’A. brassicicola sur les siliques basales (les plus âgées) et apicales (les plus jeunes présentes sur la hampe florale au moment de l’inoculation). Après quelques jours, des symptômes nécrotiques apparaissent sur les siliques, qui ont été récoltées 18 jours après inoculation. Le pathosystème mis au point va permettre l’évaluation du taux de transmission d’A. brassicicola aux semences de colza, mais aussi le décryptage du dialogue moléculaire plante-pathogène au cours de la phase de transmission aux semences.
ano.nymous@ccsd.cnrs.fr.invalid (Agathe Cailleau) 31 Jul 2024
https://hal.inrae.fr/hal-04665483v1
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[hal-04688341] The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings
Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact‐dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed‐to‐seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB , abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild‐type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS‐deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomona s genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris .
ano.nymous@ccsd.cnrs.fr.invalid (Tiffany Garin) 05 Sep 2024
https://hal.inrae.fr/hal-04688341v1
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[hal-04852994] Le microbiote des plantes - De son rôle dans la survie végétale à son ingénierie pour une agriculture durable
La majorité des êtres vivants pluricellulaires sont colonisés par une multitude de micro-organismes. C’est le cas notamment des plantes, dont les racines abritent une vaste biodiversité microbienne. Ce microbiote est composé de diverses espèces de bactéries, champignons et protistes, qui étendent le répertoire génétique de la plante, interagissent et contribuent à sa survie. Des recherches récentes illustrent l’importance du microbiote pour la santé des plantes et une agriculture durable.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 21 Dec 2024
https://hal.inrae.fr/hal-04852994v1
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[hal-03299428] Transmission of Seed and Soil Microbiota to Seedling
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa.
ano.nymous@ccsd.cnrs.fr.invalid (Aude Rochefort) 25 Oct 2021
https://hal.inrae.fr/hal-03299428v1
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[hal-03299446] Seed microbiota revealed by a large-scale meta-analysis including 50 plant species
Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 26 Jul 2021
https://hal.inrae.fr/hal-03299446v1
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[hal-04688330] Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype
<div><p>Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) under in vitro conditions. The SynComs were composed of highly abundant and prevalent, sub-dominant, or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities using gyrB gene amplicon sequencing and assessed their impacts on germination and seedling phenotype. All strains and Syn-Coms successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings. Stenotrophomonas rhizophila became dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness. Most individual strains had no effect on seedling phenotypes, with the exception of Pseudomonas viridiflava and Paenibacillus sp. which had detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina) were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa. Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 04 Sep 2024
https://hal.inrae.fr/hal-04688330v1
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[hal-04973215] Fungal Oligopeptide Transporters have different substrate specificities despite their high sequence identity.
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ano.nymous@ccsd.cnrs.fr.invalid (Carmen Becerra-Rodríguez) 02 Mar 2025
https://hal.inrae.fr/hal-04973215v1
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[hal-04670942] Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon
Background: Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. Results: In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. Conclusions: The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Quiroz Monnens) 13 Aug 2024
https://hal.inrae.fr/hal-04670942v1
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[hal-04338621] A novel “ceasefire” model to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean
Summary Although seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored. A multi-omic approach ( i.e. dual RNAseq, plant small RNAs and methylome) was performed at different seed developmental stages of common bean ( Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans ( Xcf ). In this condition, Xcf did not produce disease symptoms, neither affect seed development. Although, an intense molecular dialogue, via important transcriptional changes, was observed at the early seed developmental stages with down-regulation of plant defense signal transduction, via action of plant miR, and upregulation of the bacterial Type 3 Secretion System. At later seed maturation stages, molecular dialogue between host and pathogen was reduced to few transcriptome changes, but marked by changes in DNA methylation of plant defense and germination genes, in response to Xcf colonization, potentially acting as defense priming to prepare the host for the post-germination battle. This distinct response of infected seeds during maturation, with a more active role at early stages refutes the widely diffused assumption considering seeds as passive carriers of microbes. Finally, our data support a novel plant-pathogen interaction model, specific to the seed tissues, which differs from others by the existence of distinct phases during seed-pathogen interaction with seeds first actively interacting with colonizing pathogens, then both belligerents switch to more passive mode at later stages. We contextualized this observed scenario in a novel hypothetical model that we called “ceasefire”, where both the pathogen and the host benefit from temporarily laying down their weapons until the moment of germination.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 14 Jan 2025
https://hal.inrae.fr/hal-04338621v1
